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Estimated time of infection vs. confirmed infections

Following the ideas from Tomas Pueyo's Medium post "Coronavirus: Why You Must Act Now" [1], we assume the average time from infection to death at 23 days [2]. The data is pulled from the COVID-19 Data Repository by Johns Hopkins CSSE [3] every hour. Countries with a minimnum of 1000 confirmed cases and 40 confirmed deaths are included in this analysis.

The time from infection to death is equal to the incubation period plus the time from symptoms to death. This is used to estimate the time of the infections that lead to the observed deaths. We take the last fatality rate per country (total_cases/total_deaths) to estimate the number of infections that are responsible for the observed deaths.

In the figures below, you can observe successive waves of infections (dashed), detections (black) and deaths (red) for each country. The upper panel shows the absolute number of events. The dashed lines show the estimated number of infections. The lower panel shows the normalized number of events. Here the temporal delay between the waves and the relative change between each other can be observed.

[1] https://medium.com/@tomaspueyo/coronavirus-act-today-or-people-will-die-f4d3d9cd99ca

[2] https://github.com/midas-network/COVID-19/tree/master/parameter_estimates/2019_novel_coronavirus

[3] https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data/csse_covid_19_time_series

US
Brazil
India
Mexico
Peru
Russia
United Kingdom
Italy
Colombia
France
Argentina
Indonesia
Germany
Iran
Spain
Poland
South Africa
Ukraine
Turkey
Chile
Romania
Ecuador
Czechia
Hungary
Philippines
Canada
Belgium
Pakistan
Bangladesh
Tunisia
Iraq
Bulgaria
Netherlands
Bolivia
Portugal
Egypt
Japan
Paraguay
Sweden
Greece
Slovakia
Switzerland
Austria
Guatemala
Jordan
Nepal
Morocco
Bosnia and Herzegovina
Burma
Malaysia
Croatia
Saudi Arabia
Lebanon
Honduras
Serbia
Panama
Afghanistan
Israel
Moldova
Uruguay
Kazakhstan
Georgia
North Macedonia
Ireland
Costa Rica
Azerbaijan
Thailand
China
Armenia
Sri Lanka
Slovenia
Lithuania
Ethiopia
Algeria
Dominican Republic
Kenya
Oman
West Bank and Gaza
Venezuela
Zimbabwe
Libya
Belarus
Zambia
Namibia
Sudan
Cuba
Uganda
El Salvador
Latvia
Denmark
Albania
Kyrgyzstan
Kuwait
Kosovo
Nigeria
South Korea
United Arab Emirates
Syria
Malawi
Montenegro
Botswana
Mozambique
Cambodia
Bahrain
Senegal
Cameroon
Vietnam
Estonia
Jamaica
Trinidad and Tobago
Congo (Kinshasa)
Angola
Finland
Madagascar
Australia
Uzbekistan
Ghana
Luxembourg
Mongolia
Somalia
Rwanda
Norway
Taiwan*
Eswatini
Suriname
Qatar
Mauritania
Haiti
Guyana
Mali
Malta
Cyprus
Lesotho
Belize
Cote d'Ivoire
Cabo Verde
Bahamas
Fiji
Maldives
Guinea
Hong Kong
Papua New Guinea
Congo (Brazzaville)
Burkina Faso
Gabon
Djibouti
Togo
Andorra
Tajikistan
South Sudan

Ahead of the curve

Some countries start testing the population earlier in the outbreak than others. The time delay between the wave of deaths and the wave of confirmed cases is indicative for how early a country is detecting new cases ahead of the increase of deaths. Earlier detection means a better chances for successful isolation of an infected person and treatment of the desease.

We measure the distance of the maximum of cumulative deaths and new deaths to the number of infections to estimate the progression of the infection across countries.

If, in the early phase of the infection wave, the number of deaths rises faster than the number of confirmed cases, the distance drops, indicating that

A comparison of countries with respect to their mean time for reponse is presented below.

To determine the above values, we plot the number of confirmed cases (solid black lines) and the number of deaths (dashed black lines). From this, we measure the distance of the day of maximum deaths (dashed red lines) to the day of confirmed cases at this y-value.

The distance is indicative for how fast the humber of confirmed cases increases comapred to the increase of the number of deaths.

US
Brazil
India
Mexico
Peru
Russia
United Kingdom
Italy
Colombia
France
Argentina
Indonesia
Germany
Iran
Spain
Poland
South Africa
Ukraine
Turkey
Chile
Romania
Ecuador
Czechia
Hungary
Philippines
Canada
Belgium
Pakistan
Bangladesh
Tunisia
Iraq
Bulgaria
Netherlands
Bolivia
Portugal
Egypt
Japan
Paraguay
Sweden
Greece
Slovakia
Switzerland
Austria
Guatemala
Jordan
Nepal
Morocco
Bosnia and Herzegovina
Burma
Malaysia
Croatia
Saudi Arabia
Lebanon
Honduras
Serbia
Panama
Afghanistan
Israel
Moldova
Uruguay
Kazakhstan
Georgia
North Macedonia
Ireland
Costa Rica
Azerbaijan
Thailand
China
Armenia
Sri Lanka
Slovenia
Lithuania
Ethiopia
Algeria
Dominican Republic
Kenya
Oman
West Bank and Gaza
Venezuela
Zimbabwe
Libya
Belarus
Zambia
Namibia
Sudan
Cuba
Uganda
El Salvador
Latvia
Denmark
Albania
Kyrgyzstan
Kuwait
Kosovo
Nigeria
South Korea
United Arab Emirates
Syria
Malawi
Montenegro
Botswana
Mozambique
Cambodia
Bahrain
Senegal
Cameroon
Vietnam
Estonia
Jamaica
Trinidad and Tobago
Congo (Kinshasa)
Angola
Finland
Madagascar
Australia
Uzbekistan
Ghana
Luxembourg
Mongolia
Somalia
Rwanda
Norway
Taiwan*
Eswatini
Suriname
Qatar
Mauritania
Haiti
Guyana
Mali
Malta
Cyprus
Lesotho
Belize
Cote d'Ivoire
Cabo Verde
Bahamas
Fiji
Maldives
Guinea
Hong Kong
Papua New Guinea
Congo (Brazzaville)
Burkina Faso
Gabon
Djibouti
Togo
Andorra
Tajikistan
South Sudan